On 6/19/13 9:46 AM, Revthi Sanker wrote:
​Dear all,
I found a paper where they have updated
the c36 forcefield to include cholesterol parameters ( to which I should be
able to modify by adding an oleate chain to get my cholesteryl oleate
moiety) :
http://pubs.acs.org/doi/pdf/10.1021/jp207925m
and I found this link:
http://lists.gromacs.org/pipermail/gmx-users/2010-October/054515.html and
further obtained the file: toppar_all36_lipid_cholesterol.str
file. Should I try converting *.str file to an itp file that is compatible with
gromacs or can I add this as a new molecule to the existing lipids.rtp
in the charmm36.ff folder? Which would be a cleaner way of doing it? I
am unable to decide in this regard. Kindly provide me your valuable
suggestions.
It doesn't really matter which way you go. The "cleaner" way depends on what
type of coordinate file you have already. If you have a pre-built configuration
with molecules whose atoms conform to the force field expectations (atom names
and presence of hydrogens), I'd say just make an .itp file. If you need to
construct hydrogen positions, build .rtp and .hdb files.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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